[gmx-users] Re: 2. protein in dppc (edmund lee)
Gerrit Groenhof
ggroenh at gwdg.de
Tue Feb 23 09:08:19 CET 2010
Hi,
If I am allowed to do some advertisement:
you could try the tool g_membed for inserting proteins as well
http://wwwuser.gwdg.de/~ggroenh/membed.html
Gerrit
gmx-users-request at gromacs.org wrote:
> 2. protein in dppc (edmund lee)
>
> Date: Tue, 23 Feb 2010 15:55:36 +0800
> From: edmund lee <eyemnoob2008 at hotmail.com>
> Subject: [gmx-users] protein in dppc
> To: <gmx-users at gromacs.org>
> Message-ID: <SNT122-W306118246354907DD2561EDD420 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Justin and all..
> I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC tutorials but I am using my own protein instead.
> I had successfully reached the step INFLATEGRO where 2 lipid removed from the upper layer n 2 lipids removed from the lower layer. Then i updated my topology with deducted 4 number of molecule of lipid.
> then I generated the strong_porse.itp using the following command:
> genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> here is how the strong_posre.itp file look like[ position_restraints ]; i funct fcx fcy fcz 1 1 100000 100000 100000 2 1 100000 100000 100000 3 1 100000 100000 100000 4 1 100000 100000 100000 5 1 100000 100000 100000................3483 1 100000 100000 1000003484 1 100000 100000 1000003485 1 100000 100000 1000003486 1 100000 100000 100000
> then i updated the topology (as shown below)
> ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
> ; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include "strong_posre.itp"#endif
> ; Include DPPC chain topology#include "dppc.itp"
> ; Include water topology#include "spc.itp"
> ; System specifications[ system ]128-Lipid DPPC Bilayer
> [ molecules ]; molecule name nr.DPP 124SOL 3655
>
>
>
> and I also add in the "define" line in the energyminimization.mdp file
> here is my em.mdp file
> define =-DSTRONG_POSRESintegrator = steepnsteps = 200constraints = noneemtol = 1000.0nstcgsteep = 10 ; do a steep every 10 steps of cgemstep = 0.01 ; used with steepnstcomm = 1coulombtype = PMEns_type = gridrlist = 1.0rcoulomb = 1.0rvdw = 1.4Tcoupl = noPcoupl = nogen_vel = nonstxout = 0 ; write coords every # stepoptimize_fft = yes
>
> HOWEVER, I get this error when I proceed to the grompp step.
> Fatal error:Syntax error - File strong_posre.itp, line 3Last line read:'[ position_restraints ]'Invalid order for directive position_restraints
> Can anyone guide me in this?Yr comments and advices are appreciated.
> best regards
> edmund
> _________________________________________________________________
>
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